From 232430a15c2067bc8599d9b97ec8367b96600367 Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Mon, 10 Aug 2026 16:29:15 -0700 Subject: [PATCH 1/3] update readme with pip installation instructions --- README.rst | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/README.rst b/README.rst index 655d222..749ba19 100644 --- a/README.rst +++ b/README.rst @@ -44,7 +44,7 @@ For more information about the pyobjcryst library, please consult our `online do complex modeling initiative which originated in the DANSE project at Columbia University. It was further developed at Brookhaven National Laboratory, and Columbia University and the European Synchrotron Radiation Source (ESRF) and is now -maintained at Columbia and ESRF. +maintained at University of California and ESRF. The pyobjcryst sources are hosted at https://github.com/diffpy/pyobjcryst. Citation @@ -74,26 +74,22 @@ The second paper describes the c++ crystallographic objects in Installation ------------ -The latest release of ``pyobjcryst`` runs in python versions 3.11, 3.12 and 3.13. You may +The latest release of ``pyobjcryst`` runs in python versions 3.12, 3.13 and 3.14. You may specify an earlier release if you need it to run in an earlier version of Python. The preferred method is to use `Miniconda Python `_ -or `mamba `__ and install from the "conda-forge" channel of Conda packages. -mamba works in the same way as conda but has the advantage of being much -faster when resolving dependencies during installation. It also uses by -default the conda-forge repository, which is what almost all users would want. -To add "conda-forge" to the conda channels, run the following in a terminal. :: +To permanently add "conda-forge" to the conda channels (recommended), run the following in a terminal. :: conda config --add channels conda-forge We want to install our packages in a suitable conda environment. -The following creates and activates a new environment named ``pyobjcryst_env`` :: +The following creates and activates a new environment named ``pyobjcryst-env`` :: - conda create -n pyobjcryst_env pyobjcryst - conda activate pyobjcryst_env + conda create -n pyobjcryst-env pyobjcryst + conda activate pyobjcryst-env To confirm that the installation was successful, type :: @@ -101,13 +97,14 @@ To confirm that the installation was successful, type :: The output should print the latest version displayed on the badges above. -To use mamba, replace ``conda`` with ``mamba`` in the commands above. - pyobjcryst is also included in the ``diffpy.cmi`` collection of packages for structure analysis and so can be installed by :: conda install -c conda-forge diffpy.cmi +and following the instructions in the `diffpy.cmi documentation `_ to install packs containing pyobjcryst +and its libraries. + Optional graphical dependencies for jupyter notebooks ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Some of the classes can produce graphical outputs, which can be @@ -131,10 +128,17 @@ Alternative methods of installation These approaches are not recommended but reproduced here for advanced users. You can use ``pip`` to download and install the latest release from `Python Package Index `_. -To install using ``pip`` into your ``pyobjcryst_env`` environment, type :: +Pyobjcryst can be installed from pip. We recommend installing the dependencies that can be +found in ``requirements/conda.txt`` from conda-forge, e.g., :: + + conda create -n pyobjcryst-env python=3.14 + conda activate pyobjcryst-env + conda install -c conda-forge numpy libobjcryst libboost-devel libboost-python packaging ipywidgets matplotlib-base ipympl py3dmol pip install pyobjcryst +To install using ``pip`` into your ``pyobjcryst_env`` environment, type :: + If you prefer to install from sources, after installing the dependencies, obtain the source archive from `GitHub `_. Once installed, ``cd`` into your ``pyobjcryst`` directory and run the following :: From e208426ca51cbc2452b28c1665612e67b6db9425 Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Mon, 10 Aug 2026 16:32:42 -0700 Subject: [PATCH 2/3] news --- news/doc-readme.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 news/doc-readme.rst diff --git a/news/doc-readme.rst b/news/doc-readme.rst new file mode 100644 index 0000000..f40fd3d --- /dev/null +++ b/news/doc-readme.rst @@ -0,0 +1,23 @@ +**Added:** + +* No news added: tweak to readme + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* From b5e7387911ccf60964ff0fedc73905ea0f35671c Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Mon, 10 Aug 2026 16:39:12 -0700 Subject: [PATCH 3/3] small edits --- README.rst | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/README.rst b/README.rst index 749ba19..9472e39 100644 --- a/README.rst +++ b/README.rst @@ -44,7 +44,7 @@ For more information about the pyobjcryst library, please consult our `online do complex modeling initiative which originated in the DANSE project at Columbia University. It was further developed at Brookhaven National Laboratory, and Columbia University and the European Synchrotron Radiation Source (ESRF) and is now -maintained at University of California and ESRF. +maintained at University of California, Santa Barbara and ESRF. The pyobjcryst sources are hosted at https://github.com/diffpy/pyobjcryst. Citation @@ -137,8 +137,6 @@ found in ``requirements/conda.txt`` from conda-forge, e.g., :: conda install -c conda-forge numpy libobjcryst libboost-devel libboost-python packaging ipywidgets matplotlib-base ipympl py3dmol pip install pyobjcryst -To install using ``pip`` into your ``pyobjcryst_env`` environment, type :: - If you prefer to install from sources, after installing the dependencies, obtain the source archive from `GitHub `_. Once installed, ``cd`` into your ``pyobjcryst`` directory and run the following ::